Using the tapestriR package, we explore single nucleotide variants (SNVs), copy number variations (CNVs), and protein expression from the same single cells to obtain the only commercially available genotype-to-phenotype multi-omics data.
SNV + CNV analysis is done from experiments using the Mission Bio Tapestri Platform and reagents. More details on SNV + CNV analysis can be found in the CNV Application Note.
SNV + CNV + protein analysis adds on the Tapestri Protein Staining Protocol upstream of the Tapestri workflow. More details on SNV + CNV + protein analysis can be found in the Proteins Application Note.
The tapestriR package is an exploratory data analysis tool to discover gene-level and/or chromosome-level amplifications and deletions, including loss of heterozygosity (LOH) for CNV analysis. In addition, the tapestriR package quantifies protein expression from multiple protein targets and correlates it to SNVs and/or clones.
Instructions on how to download, install, and use the package are provided below.
If you have any feedback or questions regarding the content of this document or the provided scripts, contact Mission Bio Support at email@example.com.
This guide is intended for users with access to the Tapestri Instrument and Tapestri Pipeline software.
To use the R package, the hardware requirements are:
Minimum of 8GB of RAM, 16GB highly recommended
The following software/packages need to be installed to use these R scripts:
Important: tapestriR does not support R 4.0.0.
1. Install R
Install R version 3.6 or later. We recommend RStudio. Open R or RStudio, and execute these commands to install all the required packages:
Install `devtools` first, and then install the other packages. `devtools` attempts to automatically install the prerequisites for these packages.
install.packages(c("devtools", "hdf5r", "digest"))
Important: Install each package independently because the install script may prompt you to update previously downloaded packages.
if (!requireNamespace("BiocManager", quietly = TRUE))
2. Install the tapestriR package
Download the tapestriR package from the Tapestri Portal, and then install it as a local package.
Type in the path to the .zip file before installation:
devtools::install_local(path = "tapestri_1.1.0.tar.gz", repos='http://cran.us.r-project.org', upgrade="never")
View the package contents:
Three demo datasets are available to test the tapestriR package for SNV, CNV, and protein multi-omics data analysis.
4 cell line mix for multi-omics analysis that was processed with the Tapestri Single-Cell DNA AML Panel and a 10 oligo-conjugated protein panel. The vignette for this analysis can be found here and the dataset here.
Instructions on how to process these datasets are also included in the R package in the “inst” folder. The datasets are available on the Tapestri Portal. Each of the above-mentioned datasets contains the 4 or 5 files needed to run the R package.
If you would like to run data from your own panels/runs, download the following files from your Tapestri runs:
|Amplicon .bed||amplicons.bed*||Panel .zip file used for data processing on Tapestri DNA Pipeline|
|ADT counts for protein||example.counts.tsv||Tapestri Pipeline account|
Can be 1, 2, or 8 files
|Tapestri Pipeline account|
|VCF header||example.vcf_header.txt||Tapestri Pipeline account|
|Loom||example.loom||Tapestri Pipeline account|